Microbiome Data Visualization

Do you know how to read .qza file?

## Reading and exploring Artifacts (.qza)
SVs <- read_qza(file = "data/feature_table.qza", tmp = "data/tmpdir", rm = TRUE)

SVs$data[1:4,1:4]

otu_table(q2_ps)[1:4,1:4]

## Reading metadata
read_q2metadata("data/sample_metadata.tsv")[1:5, 1:5]

read_tsv("data/sample_metadata.tsv", comment = "#q2:types", show_col_types = FALSE)[1:5, 1:5] %>% 
  rename(SampleID="#SampleID")

## Reading taxonomy
taxonomy<-read_qza("data/taxonomy.qza")
head(taxonomy$data)

## Parse tidy taxonomy only
taxonomy<-parse_taxonomy(taxonomy$data)
head(taxonomy)



Citation

Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.


References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4



Appendix

Project main tree

.
├── LICENSE
├── README.md
├── Shannon_by_time.pdf
├── Shannon_by_time.png
├── Shannon_by_time.svg
├── VennDiagram.2023-04-08_16-21-47.log
├── VennDiagram.2023-04-08_16-24-08.log
├── config
│   ├── config.yml
│   ├── pbs
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   ├── samples.tsv
│   ├── slurm
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   └── units.tsv
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── features.csv
│   ├── metadata.csv
│   ├── metadata.tsv
│   ├── q2_demo_ps.rds
│   ├── q2_ps.rds
│   ├── shannon.csv
│   └── taxonomy.csv
├── figures
│   ├── shannon_by_time.pdf
│   ├── shannon_by_time.png
│   ├── shannon_by_time.svg
│   ├── venn_metadata_shannon.pdf
│   ├── venn_metadata_shannon.png
│   └── venn_metadata_shannon.svg
├── images
│   ├── bkgd.png
│   ├── coders.png
│   ├── ml.png
│   ├── smkreport
│   │   └── screenshot.png
│   └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── resources
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── environment.yml
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── barplot.rst
    │   ├── boxplots.rst
    │   ├── hcluster.rst
    │   ├── heatmaps.rst
    │   ├── nmds.rst
    │   ├── pcaordi.rst
    │   ├── pcoaordi.rst
    │   ├── scatter.rst
    │   ├── shannon_metadata_venn.rst
    │   ├── shannon_time_diversity.rst
    │   └── workflow.rst
    ├── rules
    │   ├── qiime2_viz.smk
    │   ├── render_index.smk
    │   ├── rmd_report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── UntitledRMD.Rmd
        ├── common.R
        ├── convert_qiime2csv.R
        ├── import_qiime2_data.R
        ├── plot_shannon_diversity.R
        ├── plot_venn_metadata_shannon.R
        ├── qiime2R.R
        ├── qiime2_phyloseq_object.R
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        └── tree.sh

16 directories, 76 files


Unlocking working directory.
Building DAG of jobs...
Creating report...
Adding venn_metadata_shannon.svg (0.17 MB).
Missing metadata for file figures/venn_metadata_shannon.svg. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
WorkflowError:
File figures/line_shannon_by_time.svg marked for report but does not exist.
[0408/175759.045573:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0408/175759.049329:ERROR:file_io.cc(91)] ReadExactly: expected 8, observed 0
[0408/175759.053703:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0408/175805.956533:INFO:headless_shell.cc(653)] Written to file /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png.
Created 1 file(s):
    /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png


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